Article
Biochemical Research Methods
Yuhui Hong, Sujun Li, Christopher J. Welch, Shane Tichy, Yuzhen Ye, Haixu Tang
Summary: 3DMolMS is a deep neural network model that predicts mass spectra from the 3D conformations of compounds. It achieved an average cosine similarity of 0.691 and 0.478 with experimental MS/MS spectra in positive and negative ion modes, respectively. The model can be fine-tuned to predict spectra acquired by different labs and instruments. Additionally, the molecular representation learned by 3DMolMS can enhance the prediction of chemical properties such as elution time and collisional cross section.
Article
Chemistry, Analytical
Ian Oesterle, Manuel Pristner, Sabrina Berger, Mingxun Wang, Vinicius Verri Hernandes, Annette Rompel, Benedikt Warth
Summary: Polyphenols, abundant in plants and fungi, have beneficial bioactive properties. High-resolution mass spectrometry (HRMS) is favored for analyzing their complexity. This study evaluated the advantages of HRMS, using untargeted techniques and online resources, for annotating polyphenols and other molecules. Despite the sensitivity loss compared to low-resolution mass spectrometry (LRMS), HRMS is capable of comprehensively investigating human polyphenol exposure, linking it to human health effects and toxicological mixture effects with other xenobiotics.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang, Changbin Yu
Summary: In this study, a novel deep learning-based model called 3D-MSNet was proposed for untargeted feature extraction in metabolomics research. Comparisons with nine popular software demonstrated that 3D-MSNet outperformed others in feature detection and quantification accuracy. Additionally, 3D-MSNet exhibited high feature extraction robustness and could be applied to profile MS data acquired with various high-resolution mass spectrometers.
Review
Biochemical Research Methods
Sven Heiles
Summary: Metabolomics and lipidomics are driving forces in the omics era, with tandem mass spectrometry methods playing a crucial role in characterizing the structural details of metabolites and lipids. Recent advancements in alternative tandem MS methodologies aim to provide full structural characterization of these compounds. The review critically examines the principles, capabilities, drawbacks, and initial applications of these advanced tandem mass spectrometry strategies in the fields of metabolomics and lipidomics.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Xiangyu Guo, Wenbo Cao, Xiaomin Fan, Zhiying Guo, Donghui Zhang, Haoyue Zhang, Xiaoxiao Ma, Jiahong Dong, Yunfang Wang, Wenpeng Zhang, Zheng Ouyang
Summary: Mass spectrometry imaging (MSI) of lipids in biological tissues can provide valuable information for biological research and disease diagnosis by correlating molecular distribution with pathological results. A new multiplexed MS2 imaging method (MSI-I-2) has been developed, allowing for MS2 images of 10 or more lipid species at each sampling spot, providing spatial structural lipidomic information. Coupled with on-tissue photochemical derivatization, imaging of 20 phospholipid C=C location isomers is also possible, resulting in enhanced molecular images with high structural definition for mouse brain and human liver cancer tissue sections. Spatially mapped t-distributed stochastic neighbor embedding has been utilized to visualize the tumor margin with the assistance of structural lipidomic information.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Xue Tian, Sheng Yang, Qu Tang, Huoyan Ji, Lei Shen, Jianxin Wang
Summary: This paper presents a liquid chromatography-tandem mass spectrometry method for the absolute quantification of serum RBP4 with high sensitivity and specificity. The method includes a series of procedures for sample preparation and separation, followed by quantitative analysis using a mass spectrometer. The results demonstrate that the method is accurate and reliable, conforming to guidelines for bioanalytical method validation.
ANALYTICAL BIOCHEMISTRY
(2022)
Review
Food Science & Technology
Clara Sousa
Summary: Natural pigments are widely distributed molecules in nature and play a significant role in our daily lives. In addition to their colors, they also have relevant biological properties associated with health benefits. Edible plant leaves, although less known as a source of natural pigments, contain a high variety of chlorophylls, carotenoids, and anthocyanins. This review critically analyzes the workflow used to identify and quantify these pigments in edible plant leaves using tandem mass spectrometry. Consistency issues in the methods used to extract and analyze these compounds are addressed. Mass spectrometry is a widely employed technique in metabolomics and will be discussed in the context of pigment identification and quantification.
Review
Biochemistry & Molecular Biology
Laura K. Meredith, Malak M. Tfaily
Summary: Microbial metabolomic studies have focused mainly on nonvolatile metabolites, neglecting the volatile organic compounds (VOCs) that play important roles in microbial systems. Advances in VOC detection allow real-time observation and overcome sampling limitations, leading to a more comprehensive understanding of microbial processes when integrating VOC and other 'omics approaches.
TRENDS IN MICROBIOLOGY
(2022)
Article
Medical Laboratory Technology
Jordi Farre-Segura, Neus Fabregat-Cabello, Chiara Calaprice, Laurent Nyssen, Stephanie Peeters, Caroline Le Goff, Etienne Cavalier
Summary: A rapid and specific LC-MS/MS method for glucagon quantitation has been developed and validated, showing stability and accuracy in comparison to other immunoassay methods. This method could potentially establish a standardized approach for glucagon analysis in routine care settings.
CLINICA CHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Prasad Phapale, Andrew Palmer, Rose Muthoni Gathungu, Dipali Kale, Britta Brugger, Theodore Alexandrov
Summary: EMBL-MCF is an open LC-MS/MS spectral library with over 1600 fragmentation spectra from 435 authentic standards of endogenous metabolites and lipids. It features chromatographic profiles acquired with different LC-MS methods and coverage of different adduct ions. The library contains many biologically important metabolites and unique metabolites and lipids compared to other public libraries.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Medicinal
Oliver Fiehn, Parker Ladd Bremer, Arpana Vaniya, Tobias Kind, Shunyang Wang
Summary: CFM-ID is a machine learning tool for predicting MS/MS spectra of metabolites. Matching experimental collision energy with CFM-ID's predicted energy produced optimal results, especially for benzenoids on HCD-Orbitrap instruments. CFM-ID 4.0 could be useful as a supplementary tool in the broader context of identification workflows.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Analytical
Lauren M. Bishop, Tong Shen, Oliver Fiehn
Summary: Accurate and reproducible quantification of endogenous lipids is crucial for large-scale lipidomic analyses. Many lipids in liquid chromatography-electrospray ionization-mass spectrometry form various adducts with buffer components, and the mechanisms and conditions affecting adduct formation are poorly understood. Variations in adduct ratios can lead to significant inaccuracies during quantification, and the use of multiple adduct ions improves accuracy compared to using a single adduct ion.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Anca-Narcisa Neagu, Madhuri Jayathirtha, Emma Baxter, Mary Donnelly, Brindusa Alina Petre, Costel C. Darie
Summary: Mass spectrometry enables the analysis of proteins and peptides, including identification of mass, amino acid sequence, and post-translational modifications. In biomedical research, mass spectrometry can be used to identify relevant biomarkers for diagnostic and therapeutic purposes.
Article
Chemistry, Multidisciplinary
Mahnoor Zulfiqar, Luiz Gadelha, Christoph Steinbeck, Maria Sorokina, Kristian Peters
Summary: Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data. MAW combines tandem mass spectrometry input data pre-processing, spectral and compound database matching, computational classification, and in silico annotation to facilitate and automate complex annotation.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Simon Lagies, Roman Pichler, Georg Vladimirov, Jana Gawron, Fabian Bazner, Annabell Schreiner, Dajana Kadena, Dietmar A. Plattner, Soeren S. Lienkamp, Bernd Kammerer
Summary: Research has found that the concentration of vancomycin in the kidneys far exceeds plasma levels, potentially leading to nephrotoxic reactions. By studying animal models and cell lines, it was discovered that exposure to vancomycin resulted in metabolic and lipidomic alterations in kidney cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Linxing Yao, Emily A. Davidson, Maliha W. Shaikh, Christopher B. Forsyth, Jessica E. Prenni, Corey D. Broeckling
Summary: Short-chain fatty acids (SCFAs) are volatile fatty acids produced by gut microbial fermentation of dietary nondigestible carbohydrates. This study presents a sensitive method for quantifying SCFAs through extraction with methyl tert-butyl ether after plasma/serum acidification. The method simplifies sample preparation, reduces contamination risk, and offers potential for automated sample preparation.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Agriculture, Multidisciplinary
Chaoyu Zhai, Steven M. Lonergan, Elisabeth J. Huff-Lonergan, Logan G. Johnson, Kitty Brown, Jessica E. Prenni, Mahesh Nair
Summary: The objective of this study was to evaluate the effects of lipid peroxidation products, specifically malondialdehyde (MDA), hexenal, and 4-hydroxynonenal (HNE), on the activity of calpain-1. It was found that calpain-1 activity increased slightly after incubation with 100 mu M MDA, but not with higher concentrations of MDA. On the other hand, calpain-1 activity was lowered by hexenal and HNE at all tested concentrations. Adducts of MDA and HNE were detected on specific amino acid residues in calpain-1. These findings suggest that lipid peroxidation products can have a concentration-dependent impact on calpain-1 activity and potentially affect meat tenderness postmortem.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Katie J. Nasiatka, Harmonie M. Bettenhausen, Jacqueline M. Chaparro, Adam L. Heuberger, Jessica E. Prenni
Summary: Hops play a vital role in beer by imparting specific flavors. The demand for hoppy beers has raised expectations for stable, quality hops with unique sensory properties. This study introduces ambient mass spectrometry (AMS) as an alternative method for rapid chemical fingerprinting of hops to assess quality. The results demonstrate the potential of this approach for rapid evaluation of hops quality, which could be beneficial for quality assurance programs and rapid phenotyping of hops by producers.
JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS
(2023)
Article
Plant Sciences
Brendon M. Anthony, Jacqueline M. Chaparro, Jessica E. Prenni, Ioannis S. Minas
Summary: The manipulation of crop load in peach trees affects carbon supply and the balance between fruit yield and quality. This study assessed the impact of carbon supply on peach fruit quality at different development stages and found that carbon-sufficient fruit had higher quality attributes. The analysis of the fruit's secondary metabolite profile revealed that early metabolic shifts primed fruit quality at harvest, and the synthesis of flavonoids was facilitated by enhanced carbon availability.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Developmental Biology
Sophie C. Walsh, Jeremy R. Miles, Corey D. Broeckling, Lea A. Rempel, Elane C. Wright-Johnson, Angela K. Pannier
Summary: This study identified potential mechanisms of porcine conceptus elongation, specifically changes in phospholipid and amino acid metabolic processes, as well as RGD-mediated elongation.
REPRODUCTION FERTILITY AND DEVELOPMENT
(2023)
Article
Food Science & Technology
Jacqueline M. Chaparro, Rachel R. Jones, Susan B. Mitchell, Corey D. Broeckling, Adam L. Heuberger, Tracy Shafizadeh, Steven Watkins, Jessica E. Prenni
Summary: Sensitive, accurate, and comprehensive assessment of mineral element and metal content in food is crucial for nutrition and food safety recommendations. However, current methods described in the literature have limitations in terms of the measured elements, application to different food matrices, and instrument accessibility. In this study, an ICP-MS method is presented for simultaneous quantification of 26 elements, and its utility is demonstrated through analysis of 100 foods from plant and animal sources. The method allows measurement of elements with concentrations varying over 6 orders of magnitude, making it an efficient option for identifying suitable foods to address mineral nutrient deficiency and possible toxic element content assessment.
ACS FOOD SCIENCE & TECHNOLOGY
(2023)
Article
Food Science & Technology
Kathryn Fromuth, Jacqueline M. Chaparro, Dana Sedin, Charlene Van Buiten, Jessica E. Prenni
Summary: In this study, a metabolomics approach was used to analyze the metabolite profiles of canned and bottled beers over a 6-month aging period. The results showed that the package type significantly impacts the stability of beer.
ACS FOOD SCIENCE & TECHNOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Valerie A. Seitz, Jacqueline M. Chaparro, Meagan E. Schipanski, Kelly C. Wrighton, Jessica E. Prenni
Summary: Cover cropping is a sustainable alternative to traditional crop rotation practices, but the impact of root exudation from different cover crop species and cultivars is still uncertain. This study used non-targeted gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), as well as targeted LC-MS/MS, to analyze the chemical composition of root exudates from 16 commonly used cover crop species and 3 distinct cultivars of hairy vetch. The results showed that root exudation profiles varied across crop species and cultivars, with legumes standing out as a unique group capable of producing diverse secondary metabolites.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Entomology
Christopher Brendan Hayes, Olivia Carter, Jacob Robert MacWilliams, Whitney Cranshaw, Jacqueline M. Chaparro, Jessica E. Prenni, Punya Nachappa
Summary: This study evaluates the relationship between hemp and hemp russet mite, and finds that high-CBD hemp varieties have a deterrent effect on mite reproduction. Additionally, sulfur sprays and hot water immersion can effectively reduce mite populations and increase hemp yield and cannabinoid production.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2023)
Article
Environmental Sciences
Victoria J. Larson, Jorge L. Rico, Lisa M. Wolfe, Sybil Sharvelle, Jessica Prenni, Susan K. De Long
Summary: This study aims to identify optimal operating conditions for the degradation of emerging contaminants, including veterinary pharmaceuticals and steroid hormones, in manure treatment. The results showed that under specific temperature, pH, and carbon source conditions, efficient degradation of certain pollutants can be achieved. Additionally, potential microorganisms that may contribute to the degradation process during the aerobic composting phase were identified from the microbial strains in the anaerobic digestion system.
JOURNAL OF ENVIRONMENTAL QUALITY
(2023)
Article
Cell Biology
G. D. Catandi, D. R. Bresnahan, S. O. Peters, K. J. Fresa, L. J. Maclellan, C. D. Broeckling, E. M. Carnevale
Summary: Many age-related changes in metabolite abundance suggest impaired mitochondrial metabolic function and oxidative stress in oocytes and follicular cells. The results also indicate impaired transfer of carbohydrate and free fatty acid substrates from cumulus cells to the oocytes of old mares, potentially related to disruption of transzonal projections between the cell types. The identification of age-associated alterations in the abundance of specific metabolites and their correlations among cells contribute to our understanding of follicular dysfunction with maternal aging.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Engineering, Environmental
Nohyeong Jeong, Marin E. E. Wiltse, Aaron Boyd, Tamzin Blewett, Shinyun Park, Corey Broeckling, Thomas Borch, Tiezheng Tong
Summary: Treatment and reuse of unconventional oil and gas (UOG) produced water are crucial to addressing water scarcity and pollution issues. This study examined the effectiveness of pretreatment followed by nanofiltration (NF) and reverse osmosis (RO) in treating UOG produced water. The results showed that the pretreatment had a minor impact, NF permeates did not meet water quality criteria, and while RO removed most contaminants, some exceeded irrigation guidelines. Thorough analysis is required to understand the feasibility and potential risks of treating UOG produced water for beneficial reuse.
ACS ES&T ENGINEERING
(2023)
Article
Food Science & Technology
Brooke Sayre-Chavez, Bridget Baxter, Corey D. Broeckling, Maria Munoz-Amatriain, Mark Manary, Elizabeth P. Ryan
Summary: This study analyzed the composition of cowpea, pigeon pea, and common bean using UPLC-MS technology. It identified several metabolites that can differentiate these legumes, with cowpea having higher abundance of novel metabolites compared to other legumes. Additionally, specific metabolite markers were found in different cowpea varieties.
FOOD CHEMISTRY: MOLECULAR SCIENCES
(2022)
Review
Endocrinology & Metabolism
Katrice A. Lippa, Juan J. Aristizabal-Henao, Richard D. Beger, John A. Bowden, Corey Broeckling, Chris Beecher, W. Clay Davis, Warwick B. Dunn, Roberto Flores, Royston Goodacre, Goncalo J. Gouveia, Amy C. Harms, Thomas Hartung, Christina M. Jones, Matthew R. Lewis, Ioanna Ntai, Andrew J. Percy, Dan Raftery, Tracey B. Schock, Jinchun Sun, Georgios Theodoridis, Fariba Tayyari, Federico Torta, Candice Z. Ulmer, Ian Wilson, Baljit K. Ubhi
Summary: This review emphasizes the importance of reference materials (RMs) and methodologies in ensuring standardization and comparability of results in untargeted metabolomics and lipidomics research. RMs are critical tools for quality control, improving the reliability and standardization of data analysis and interpretation.